Genomic Analysis of Plasmodium vivax in Southern Ethiopia Reveals Selective Pressures in Multiple Parasite Mechanisms

Sarah Auburn, Sisay Getachew, Richard D. Pearson, Roberto Amato, Olivo Miotto, Hidayat Trimarsanto, Sha Joe Zhu, Angela Rumaseb, Jutta Marfurt, Rintis Noviyanti, Matthew J. Grigg, Bridget Barber, Timothy William, Sonia Morgado Goncalves, Eleanor Drury, Kanlaya Sriprawat, Nicholas M. Anstey, Francois Nosten, Beyene Petros, Abraham Aseffa & 3 others Gil McVean, Dominic P. Kwiatkowski, Ric N. Price

    Research output: Contribution to journalArticleResearchpeer-review

    Abstract

    The Horn of Africa harbors the largest reservoir of Plasmodium vivax in the continent. Most of sub-Saharan Africa has remained relatively vivax-free due to a high prevalence of the human Duffy-negative trait, but the emergence of strains able to invade Duffy-negative reticulocytes poses a major public health threat. We undertook the first population genomic investigation of P. vivax from the region, comparing the genomes of 24 Ethiopian isolates against data from Southeast Asia to identify important local adaptions. The prevalence of the Duffy binding protein amplification in Ethiopia was 79%, potentially reflecting adaptation to Duffy negativity. There was also evidence of selection in a region upstream of the chloroquine resistance transporter, a putative chloroquine-resistance determinant. Strong signals of selection were observed in genes involved in immune evasion and regulation of gene expression, highlighting the need for a multifaceted intervention approach to combat P. vivax in the region.
    Original languageEnglish
    Pages (from-to)1738-1749
    Number of pages12
    JournalJournal of Infectious Diseases
    Volume220
    Issue number11
    Early online date21 Jan 2019
    DOIs
    Publication statusPublished - 1 Dec 2019

    Fingerprint

    Plasmodium vivax
    Ethiopia
    Parasites
    Chloroquine
    Immune Evasion
    Metagenomics
    Southeastern Asia
    Africa South of the Sahara
    Reticulocytes
    Gene Expression Regulation
    Carrier Proteins
    Public Health
    Genome
    Genes

    Cite this

    Auburn, Sarah ; Getachew, Sisay ; Pearson, Richard D. ; Amato, Roberto ; Miotto, Olivo ; Trimarsanto, Hidayat ; Zhu, Sha Joe ; Rumaseb, Angela ; Marfurt, Jutta ; Noviyanti, Rintis ; Grigg, Matthew J. ; Barber, Bridget ; William, Timothy ; Goncalves, Sonia Morgado ; Drury, Eleanor ; Sriprawat, Kanlaya ; Anstey, Nicholas M. ; Nosten, Francois ; Petros, Beyene ; Aseffa, Abraham ; McVean, Gil ; Kwiatkowski, Dominic P. ; Price, Ric N. / Genomic Analysis of Plasmodium vivax in Southern Ethiopia Reveals Selective Pressures in Multiple Parasite Mechanisms. In: Journal of Infectious Diseases. 2019 ; Vol. 220, No. 11. pp. 1738-1749.
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    abstract = "The Horn of Africa harbors the largest reservoir of Plasmodium vivax in the continent. Most of sub-Saharan Africa has remained relatively vivax-free due to a high prevalence of the human Duffy-negative trait, but the emergence of strains able to invade Duffy-negative reticulocytes poses a major public health threat. We undertook the first population genomic investigation of P. vivax from the region, comparing the genomes of 24 Ethiopian isolates against data from Southeast Asia to identify important local adaptions. The prevalence of the Duffy binding protein amplification in Ethiopia was 79{\%}, potentially reflecting adaptation to Duffy negativity. There was also evidence of selection in a region upstream of the chloroquine resistance transporter, a putative chloroquine-resistance determinant. Strong signals of selection were observed in genes involved in immune evasion and regulation of gene expression, highlighting the need for a multifaceted intervention approach to combat P. vivax in the region.",
    keywords = "Plasmodium, Duffy, Ethiopia, genomics, malaria, vivax",
    author = "Sarah Auburn and Sisay Getachew and Pearson, {Richard D.} and Roberto Amato and Olivo Miotto and Hidayat Trimarsanto and Zhu, {Sha Joe} and Angela Rumaseb and Jutta Marfurt and Rintis Noviyanti and Grigg, {Matthew J.} and Bridget Barber and Timothy William and Goncalves, {Sonia Morgado} and Eleanor Drury and Kanlaya Sriprawat and Anstey, {Nicholas M.} and Francois Nosten and Beyene Petros and Abraham Aseffa and Gil McVean and Kwiatkowski, {Dominic P.} and Price, {Ric N.}",
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    Auburn, S, Getachew, S, Pearson, RD, Amato, R, Miotto, O, Trimarsanto, H, Zhu, SJ, Rumaseb, A, Marfurt, J, Noviyanti, R, Grigg, MJ, Barber, B, William, T, Goncalves, SM, Drury, E, Sriprawat, K, Anstey, NM, Nosten, F, Petros, B, Aseffa, A, McVean, G, Kwiatkowski, DP & Price, RN 2019, 'Genomic Analysis of Plasmodium vivax in Southern Ethiopia Reveals Selective Pressures in Multiple Parasite Mechanisms', Journal of Infectious Diseases, vol. 220, no. 11, pp. 1738-1749. https://doi.org/10.1093/infdis/jiz016

    Genomic Analysis of Plasmodium vivax in Southern Ethiopia Reveals Selective Pressures in Multiple Parasite Mechanisms. / Auburn, Sarah; Getachew, Sisay; Pearson, Richard D.; Amato, Roberto; Miotto, Olivo; Trimarsanto, Hidayat; Zhu, Sha Joe; Rumaseb, Angela; Marfurt, Jutta; Noviyanti, Rintis; Grigg, Matthew J.; Barber, Bridget; William, Timothy; Goncalves, Sonia Morgado; Drury, Eleanor; Sriprawat, Kanlaya; Anstey, Nicholas M.; Nosten, Francois; Petros, Beyene; Aseffa, Abraham; McVean, Gil; Kwiatkowski, Dominic P.; Price, Ric N.

    In: Journal of Infectious Diseases, Vol. 220, No. 11, 01.12.2019, p. 1738-1749.

    Research output: Contribution to journalArticleResearchpeer-review

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    AU - Auburn, Sarah

    AU - Getachew, Sisay

    AU - Pearson, Richard D.

    AU - Amato, Roberto

    AU - Miotto, Olivo

    AU - Trimarsanto, Hidayat

    AU - Zhu, Sha Joe

    AU - Rumaseb, Angela

    AU - Marfurt, Jutta

    AU - Noviyanti, Rintis

    AU - Grigg, Matthew J.

    AU - Barber, Bridget

    AU - William, Timothy

    AU - Goncalves, Sonia Morgado

    AU - Drury, Eleanor

    AU - Sriprawat, Kanlaya

    AU - Anstey, Nicholas M.

    AU - Nosten, Francois

    AU - Petros, Beyene

    AU - Aseffa, Abraham

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    AU - Kwiatkowski, Dominic P.

    AU - Price, Ric N.

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    N2 - The Horn of Africa harbors the largest reservoir of Plasmodium vivax in the continent. Most of sub-Saharan Africa has remained relatively vivax-free due to a high prevalence of the human Duffy-negative trait, but the emergence of strains able to invade Duffy-negative reticulocytes poses a major public health threat. We undertook the first population genomic investigation of P. vivax from the region, comparing the genomes of 24 Ethiopian isolates against data from Southeast Asia to identify important local adaptions. The prevalence of the Duffy binding protein amplification in Ethiopia was 79%, potentially reflecting adaptation to Duffy negativity. There was also evidence of selection in a region upstream of the chloroquine resistance transporter, a putative chloroquine-resistance determinant. Strong signals of selection were observed in genes involved in immune evasion and regulation of gene expression, highlighting the need for a multifaceted intervention approach to combat P. vivax in the region.

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    KW - malaria

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